Curation and Characterization of a Collection of Mycobacteriophages

Bacteriophages are the most abundant biological entity on earth, with an estimated number of 1031. Bacteriophages specifically kill bacteria. Phages that infect M.smegmatis could potentially be used as an alternative to antibiotics.https://digitalcommons.mtech.edu/urp_aug_2018/1012/thumbnail.jp

Annotation of Bacteriophage BigPaolini

Bacteriophages were discovered nearly 100 years ago. With new interest in phages many phages are being analyzed and annotated to understand the diversity within the phage world.https://digitalcommons.mtech.edu/urp_aug_2018/1010/thumbnail.jp

Investigation of Genomic Deletion of Mycobacteriophage Moonbeam

Hypothesis: There are two, genomically separate Mycobacteriophages in Moonbeam lysate that was used and sent DNA template to the University of Pittsburgh in 2020. Experimental Aims: Separate and characterize phages with deletion from non-deletion phages in Moonbeam lysate

The Amplification and Characterization of Mycobacteriophages MyPhage and SolarFlare

Bacteriophages are viruses that infect and replicate in bacteria and are being researched for medical applications. MyPhage is a Mycobacteriophage discovered in Anaconda, Montana in May of 2009. The student found the phage in soil from a potted plant. The background of SolarFlare is unknown.https://digitalcommons.mtech.edu/urp_aug_2018/1003/thumbnail.jp

Digital planning of composite customized veneers using Digital Smile Design: Evaluation of its accuracy and manufacturing

Objectives: This study aimed to evaluate the production of customized composite veneers starting from a two-dimensional (2D) digital preview using the Digital Smile System (DSS). Material and Methods: A photographic examination of 30 patients was performed by taking two digital pictures of the face and a digital preview through the DSS. Moreover, optical scans of the dental arches were obtained and the data were entered into a three-dimensional (3D) software to prepare a virtual preview. The standard tessellation language files were sent for production using CAD-CAM technology. The Friedman test, Bonferroni, and Dunn post hoc tests were used, comparing the linear measurements of the 2D and 3D plans and the final veneers (α =.05). Results: Significant differences emerged between the pictures and digital scans on the mesial–distal widths of the lateral incisors and canine. Linear measurements in the 2D plan were significantly different from those of the 3D plan, except for the height measures of incisors. No significant changes were found on comparing the parameters of the 2D and 3D plans with those of the final pieces. Conclusions: The customized veneers were clinically adequate and similar to 2D and 3D plans, although significant differences emerged between the picture and digital scans as well as between the 2D and 3D plans

Facial artery myomucosal flap vs. Islanded facial artery myomucosal flap viability: A systematic review

The aim of this study was to estimate the overall viability of the islanded facial artery myomucosal flap (iFAMM) compared to the facial artery myomucosal flap (FAMM). A systematic review of English articles was performed on PubMed and Cochrane Library electronic databases. Search terms included every nomenclature variant for FAMM flap and iFAMM flap. A total of 373 articles were identified, and 20 articles were considered eligible for inclusion in the review. A total of 486 flaps were evaluated (350 FAMM and 136 i-FAMM flaps). In all studies, the primary outcome assessed was flap viability, collecting the rate of total and partial flap necrosis and then comparing FAMM to i-FAMM. Overall reported partial/total necrosis rate for FAMM flap was 9.7%, 1.4% as total and 8.3% as partial necrosis. Overall partial/total reported necrosis rate for iFAMM flaps was 2.2%, 1.5% as total and 0.7% as partial necrosis. FAMM flaps, both as classical or islanded variants, are an effective option for intraoral small/medium sized defect reconstruction. Outcomes from the present review show a higher partial/total survival rate when this flap is harvested as islanded flap

Repeatability of dental shade by digital spectrophotometry in current, former, and never smokers

Cigarette smoking contributes to poor oral health and dental discoloration. Therefore, stopping smoking may translate into measurable amelioration of dental shade indices. We compared dental shade parameters by digital spectrophotometry among current, former, and never smokers and verified their repeatability at 7 and 30 days. Dental shade parameters (CIE L*a*b* and corresponding whiteness index for dentistry-WID) were measured in current, former, and never smokers with a digital spectrophotometer (Vita Easyshade V) on three separate study visits: at baseline (day 0), at day 7, and day 30. Dental shade parameters were analyzed in 18 current, 18 former, and 20 never smokers. The repeatability of shade parameters was consistent in current, former, and never smokers. L*, a*, b*, and WID show significant short and long-term repeatability (p < 0.0001, by regression analyses). The mean (± SD) WID score of 13.42 (± 4.9) in current smokers was significantly lower compared to the WID score of 20.38 (± 5.3) in never smokers (p = 0.001). No significant differences were observed between current and former smokers and between former smokers and former smokers. Dental shade measurements by digital spectrophotometry were highly reproducible and showed that teeth whiteness of current smokers is substantially inferior compared to never smokers. Objective discrimination of dental shade can be a valuable regulatory science endpoint for investigating oral hygiene and dental aesthetics of consumer care products, smoking cessation medications, and tar-free tobacco products (e-cigarettes, heated tobacco products, oral nicotine products) for cigarette substitution. Clinical trial registration: the study was not registered in ClinicalTrials.gov considering that it is a pilot study, parts of a larger project with ID: NCT04649645

Calcium hydroxide removal using four different irrigation systems: A quantitative evaluation by scanning electron microscopy

This study compares conventional endodontic needle irrigation, passive ultrasonic irriga-tion, apical negative pressure irrigation, and mechanical activation to remove calcium hydroxide from single straight root canals. Eighty-four mandibular premolars were prepared in a crown-down manner up to size #40. Two teeth represented a negative control, and another two served as a positive control. Calcium hydroxide paste was placed inside root canals. The remaining eighty samples were analyzed based on the activation techniques, and the cleanliness of the canals was quantified using Fiji’s software on 500× magnified SEM backscattered electron micrographs. Considering the whole canal, all instruments showed better performance than conventional endodontic needle irrigation in removing calcium hydroxide (p < 0.05). Irrisafe and XP-endo Finisher could remove a significantly higher amount of calcium hydroxide than Endovac (p < 0.05). Irrisafe and XP-endo Finisher have been able to remove more calcium hydroxide than EndoVac

“Re-Culturing” Teacher Education: Inquiry, Evidence, and Action

Currently the press to make policy and practice decisions on the basis of evidence is being coupled with recognition that real change requires shifts in organizational culture. Consequently, there are now many efforts to “re-culture” organizations by making evidence central to decision making. In this article, the authors problematize the notion of a “culture of evidence” in teacher education. Then the article identifies four key aspects involved in efforts to create a culture of evidence at one institution over a five-year period: (1) development of a portfolio of studies about processes and outcomes; (2) recognition that teacher education always poses values questions as well as empirical questions; (3) an exploratory, open-ended approach to evidence construction; and, (4) multiple structures that institutionalize evidence collection and use locally and beyond. The authors suggests that building cultures of evidence has the potential to be transformative in teacher education, but only if challenges related to sustainability, complexity, and balance are addressed

Genome landscapes and bacteriophage codon usage

Across all kingdoms of biological life, protein-coding genes exhibit unequal usage of synonmous codons. Although alternative theories abound, translational selection has been accepted as an important mechanism that shapes the patterns of codon usage in prokaryotes and simple eukaryotes. Here we analyze patterns of codon usage across 74 diverse bacteriophages that infect E. coli, P. aeruginosa and L. lactis as their primary host. We introduce the concept of a `genome landscape,' which helps reveal non-trivial, long-range patterns in codon usage across a genome. We develop a series of randomization tests that allow us to interrogate the significance of one aspect of codon usage, such a GC content, while controlling for another aspect, such as adaptation to host-preferred codons. We find that 33 phage genomes exhibit highly non-random patterns in their GC3-content, use of host-preferred codons, or both. We show that the head and tail proteins of these phages exhibit significant bias towards host-preferred codons, relative to the non-structural phage proteins. Our results support the hypothesis of translational selection on viral genes for host-preferred codons, over a broad range of bacteriophages.Comment: 9 Color Figures, 5 Tables, 53 Reference